annotateDMRsWithGenes   Annotate DMRs with Gene Information
augmentBSSeq            Augment BSseq Object
buildDMRs               Build Differentially Methylated Regions (DMRs)
                        from Differentially Methylated Positions
                        (seeds)
combinePvalues          Combine spatially correlated p-values with
                        comb-p style SLK correction
computeDMRsInteraction
                        Compute Motif-Based DMR Interactions
convertBetaToTabix      Convert Beta File to Tabix-Indexed Format
extractDMRMotifs        Extract DMR Motif Frequencies
findDMPsArray           Find DMPs from methylation array beta values
                        using limma
findDMPsBSSeq           Find DMPs using DSS on BSseq objects
getBetaHandler          Create a BetaHandler object for efficient beta
                        value access
getDMRSequences         Extract DNA Sequences for DMRs
getSortedGenomicLocs    Get Sorted Array Locations
launchCMEntViewer       Launch CMEnt Interactive Viewer
loadExampleInputData    Load CMEnt Example Resources
orderByLoc              Orders a vector of indices according to their
                        corresponding genomic locations (chromosome and
                        position). This function is useful for sorting
                        site sites or other genomic features by their
                        physical positions.
plotAutoDMRsCircos      Plot DMR Circos Views Using Automatically
                        Selected Regions
plotDMR                 Plot DMR
plotDMRBlockFormation   Plot Intermediate DMR Block Formation
                        Diagnostics
plotDMRs                Plot Multiple DMRs in a Grid
plotDMRsCircos          Plot Circos Visualization of DMRs
plotDMRsManhattan       Plot Manhattan-Style View of DMR Scores
readCustomMethylationBedData
                        Read and Process Custom Methylation BED Data
reduceBSseqAroundSeeds
                        Reduce BSseq object around seed locations
scoreDMRs               Add Complementary Classification Scores to DMRs
simulateDMRs            Simulate DMRs while preserving local
                        methylation structure
sortBetaFileByCoordinates
                        Sort Beta File by Genomic Coordinates
sparsifySeeds           Sparsify seed locations by minimum distance
